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- PDB-6dio: Structure of class II HMG-CoA reductase from Delftia acidovorans ... -

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Basic information

Entry
Database: PDB / ID: 6dio
TitleStructure of class II HMG-CoA reductase from Delftia acidovorans with NAD bound
Components3-hydroxy-3-methylglutaryl coenzyme A reductase
KeywordsOXIDOREDUCTASE / Mevalonate pathway
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA reductase / hydroxymethylglutaryl-CoA reductase (NADH) activity / hydroxymethylglutaryl-CoA reductase (NADPH) activity / coenzyme A metabolic process / nucleotide binding
Similarity search - Function
Hydroxymethylglutaryl-CoA reductase, bacterial-type / Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain / 3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2 / 3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2 / Hydroxymethylglutaryl-coenzyme A reductases signature 2. / Hydroxymethylglutaryl-coenzyme A reductases signature 1. / Hydroxymethylglutaryl-coenzyme A reductases signature 3. / Hydroxymethylglutaryl-CoA reductase, class I/II / Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, substrate-binding domain superfamily ...Hydroxymethylglutaryl-CoA reductase, bacterial-type / Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain / 3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2 / 3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2 / Hydroxymethylglutaryl-coenzyme A reductases signature 2. / Hydroxymethylglutaryl-coenzyme A reductases signature 1. / Hydroxymethylglutaryl-coenzyme A reductases signature 3. / Hydroxymethylglutaryl-CoA reductase, class I/II / Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, substrate-binding domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, catalytic domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, conserved site / Hydroxymethylglutaryl-coenzyme A reductase / Hydroxymethylglutaryl-coenzyme A reductases family profile. / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / : / 3-hydroxy-3-methylglutaryl coenzyme A reductase
Similarity search - Component
Biological speciesDelftia acidovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsRagwan, E.R. / Arai, E. / Kung, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116029 United States
CitationJournal: Biochemistry / Year: 2018
Title: New Crystallographic Snapshots of Large Domain Movements in Bacterial 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase.
Authors: Ragwan, E.R. / Arai, E. / Kung, Y.
History
DepositionMay 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 17, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-hydroxy-3-methylglutaryl coenzyme A reductase
B: 3-hydroxy-3-methylglutaryl coenzyme A reductase
C: 3-hydroxy-3-methylglutaryl coenzyme A reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,83747
Polymers135,5723
Non-polymers5,26544
Water16,574920
1
A: 3-hydroxy-3-methylglutaryl coenzyme A reductase
B: 3-hydroxy-3-methylglutaryl coenzyme A reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,97832
Polymers90,3822
Non-polymers3,59730
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18480 Å2
ΔGint-98 kcal/mol
Surface area26460 Å2
MethodPISA
2
C: 3-hydroxy-3-methylglutaryl coenzyme A reductase
hetero molecules

C: 3-hydroxy-3-methylglutaryl coenzyme A reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,71830
Polymers90,3822
Non-polymers3,33728
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area19650 Å2
ΔGint-66 kcal/mol
Surface area28220 Å2
MethodPISA
3
A: 3-hydroxy-3-methylglutaryl coenzyme A reductase
B: 3-hydroxy-3-methylglutaryl coenzyme A reductase
hetero molecules

A: 3-hydroxy-3-methylglutaryl coenzyme A reductase
B: 3-hydroxy-3-methylglutaryl coenzyme A reductase
hetero molecules

C: 3-hydroxy-3-methylglutaryl coenzyme A reductase
hetero molecules

C: 3-hydroxy-3-methylglutaryl coenzyme A reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,67594
Polymers271,1456
Non-polymers10,53088
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
crystal symmetry operation6_664x-y+1,x+1,z-1/61
crystal symmetry operation8_665x-y+1,-y+1,-z1
Buried area65460 Å2
ΔGint-292 kcal/mol
Surface area72280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.000, 113.000, 437.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-889-

HOH

21A-903-

HOH

31C-704-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein 3-hydroxy-3-methylglutaryl coenzyme A reductase / HMG-CoA reductase


Mass: 45190.758 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Delftia acidovorans (bacteria) / Gene: CHL79_09160 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A291JGB7, UniProt: A9BQX8*PLUS, hydroxymethylglutaryl-CoA reductase

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Non-polymers , 5 types, 964 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 920 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium citrate, pH 5.0, 0.5 M ammonium sulfate, 0.6 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2018
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.14→98.86 Å / Num. obs: 92136 / % possible obs: 99.93 % / Redundancy: 2 % / Biso Wilson estimate: 21.39 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.0976 / Net I/σ(I): 5.4
Reflection shellResolution: 2.14→2.22 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→97.861 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.43
RfactorNum. reflection% reflection
Rfree0.2389 4723 5.13 %
Rwork0.1905 --
obs0.193 92123 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.14→97.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9085 0 333 920 10338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079530
X-RAY DIFFRACTIONf_angle_d0.90512921
X-RAY DIFFRACTIONf_dihedral_angle_d11.7146304
X-RAY DIFFRACTIONf_chiral_restr0.051512
X-RAY DIFFRACTIONf_plane_restr0.0051682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.16430.34411460.29732840X-RAY DIFFRACTION100
2.1643-2.18980.35451520.2952857X-RAY DIFFRACTION100
2.1898-2.21650.31571460.29212883X-RAY DIFFRACTION100
2.2165-2.24460.34111610.2842822X-RAY DIFFRACTION100
2.2446-2.27410.35381550.28332890X-RAY DIFFRACTION100
2.2741-2.30520.33221800.28362856X-RAY DIFFRACTION100
2.3052-2.33820.33181590.26252821X-RAY DIFFRACTION100
2.3382-2.37310.27561620.26412857X-RAY DIFFRACTION100
2.3731-2.41020.29121550.24662880X-RAY DIFFRACTION100
2.4102-2.44970.31521630.23912882X-RAY DIFFRACTION100
2.4497-2.49190.29941440.23442837X-RAY DIFFRACTION100
2.4919-2.53720.32191540.22482889X-RAY DIFFRACTION100
2.5372-2.58610.28331320.22592899X-RAY DIFFRACTION100
2.5861-2.63880.26791610.21422866X-RAY DIFFRACTION100
2.6388-2.69620.26961720.20722896X-RAY DIFFRACTION100
2.6962-2.75890.24961550.18772885X-RAY DIFFRACTION100
2.7589-2.8280.25821470.19042915X-RAY DIFFRACTION100
2.828-2.90440.27391560.17982873X-RAY DIFFRACTION100
2.9044-2.98990.24031470.18822917X-RAY DIFFRACTION100
2.9899-3.08640.25261490.19272889X-RAY DIFFRACTION100
3.0864-3.19670.23061660.20682917X-RAY DIFFRACTION100
3.1967-3.32470.23121700.17182924X-RAY DIFFRACTION100
3.3247-3.4760.19281440.15762923X-RAY DIFFRACTION100
3.476-3.65930.21091590.15042939X-RAY DIFFRACTION100
3.6593-3.88860.18861550.13992951X-RAY DIFFRACTION100
3.8886-4.18880.16291690.13112953X-RAY DIFFRACTION100
4.1888-4.61040.15951600.11732978X-RAY DIFFRACTION100
4.6104-5.27740.16971560.13243014X-RAY DIFFRACTION100
5.2774-6.64880.20031660.17473078X-RAY DIFFRACTION100
6.6488-97.96330.20591820.1793269X-RAY DIFFRACTION99

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